PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID RrC320_p2
Organism
Raphanus raphanistrum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family B3
Protein Properties Length: 775aa    MW: 85701 Da    PI: 7.3691
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC320_p2genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B357.82e-18287386198
                EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEE CS
         B3   1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkv 96 
                f+kvl+ sd+++ grlvlpk +ae++   ++++e+  l+++d +g++W +++++  +++s++yvl+ G     ++ +L++gD+v+F++++  e++lv++ 
  RrC320_p2 287 FEKVLSASDAGRIGRLVLPKACAEAYfpPISQPEGLPLKIQDIKGKEWVFQFRFwpNNNSRMYVLE-GVTPCIQSMQLQAGDTVTFSRTE-PEGKLVMGY 384
                99**************************555566778***************9989999999***9.********************654.777777776 PP

                E- CS
         B3  97 fr 98 
                ++
  RrC320_p2 385 RK 386
                65 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.105.4E-30281390IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019366.02E-20284387IPR015300DNA-binding pseudobarrel domain
CDDcd100171.64E-22285386No hitNo description
PROSITE profilePS5086311.053287388IPR003340B3 DNA binding domain
SMARTSM010194.9E-20287387IPR003340B3 DNA binding domain
PfamPF023621.3E-15287386IPR003340B3 DNA binding domain
PROSITE profilePS5105014.8516566IPR011124Zinc finger, CW-type
PfamPF074968.5E-13521563IPR011124Zinc finger, CW-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0010030Biological Processpositive regulation of seed germination
GO:2000034Biological Processregulation of seed maturation
GO:0003677Molecular FunctionDNA binding
GO:0008270Molecular Functionzinc ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 775 aa     Download sequence    Send to blast
MESTKVCMNA QCGSTTSTSG EWKRGWPMRS GELASLCDKC GSAYEQSIFC QVFHAEESGW  60
RECSSCDKRL HCGCIASRFM MELLDNGGVT CISCAKKSGL FYMNVCHETN GRDFPTFASA  120
EHISSVLERT NLKHLLHFQR ISPTQPFLQM KQEESLLPAR LDPLRHKKES QESSAHPNLS  180
ISLGPTLMTS LPFHDAAVVV DDRSKTTPVF QLASSRSRQL LPKPANSAPA PVESSIVSQI  240
HVARPPPEGR GKTQLLPRYW PRITDQELQQ LSGQYPHLSN SKIVPLFEKV LSASDAGRIG  300
RLVLPKACAE AYFPPISQPE GLPLKIQDIK GKEWVFQFRF WPNNNSRMYV LEGVTPCIQS  360
MQLQAGDTVT FSRTEPEGKL VMGYRKATNS TASQMFKGSS EPNLNMFSNN LSSGCGDINW  420
SKLDKSEDMS KDSLLLQPSL ISARKRVRNI GTKSKRLLID SVDVLELRLT WEEAQELLRP  480
PQSAKPSICT VEDHDFEEYD EPPVFGKRTV FVSRQTGEQE QWVQCDACAK WRRLPVDTLL  540
PPKWLCSDNL LDPGRSSCSA PDELTPREQD TLLRLSKEFK RRRLASSNQE EASALDTLAN  600
AAITTTGEQG ETEVAATTKH PRHRAGCSCI VCSQPPSGKG KHKPSCTCTV CEAVKRRFKT  660
LMMRKRNREE AGQASQQAQS ECREETEAES VPAVELPAAA AGGNIDLNSD PASRVSMMSL  720
LQAATFPLEA YLKQKAVPNT AAEQQSSDIV STENGSSSAA QEHDRDTSGA PEALN
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A5e-672613942131B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1579583KRRRL
Functional Description ? help Back to Top
Source Description
UniProtTranscriptional repressor of gene expression involved in embryonic pathways, such as LEC1, ABI3, and FUS3. Repressor of the sugar-inducible genes involved in the seed maturation program in seedlings. Plays an essential role in regulating the transition from seed maturation to seedling growth. Functionally redundant with VAL1/HSI2. {ECO:0000269|PubMed:17158584, ECO:0000269|PubMed:17267611}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018480234.10.0PREDICTED: B3 domain-containing transcription repressor VAL2-like
RefseqXP_018480235.10.0PREDICTED: B3 domain-containing transcription repressor VAL2-like
SwissprotQ5CCK40.0VAL2_ARATH; B3 domain-containing transcription repressor VAL2
TrEMBLA0A078FMA00.0A0A078FMA0_BRANA; BnaA03g51860D protein
STRINGBra023968.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM72032639
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G32010.10.0HSI2-like 1
Publications ? help Back to Top
  1. Jia H,McCarty DR,Suzuki M
    Distinct roles of LAFL network genes in promoting the embryonic seedling fate in the absence of VAL repression.
    Plant Physiol., 2013. 163(3): p. 1293-305
    [PMID:24043445]
  2. Chhun T, et al.
    HSI2 Repressor Recruits MED13 and HDA6 to Down-Regulate Seed Maturation Gene Expression Directly During Arabidopsis Early Seedling Growth.
    Plant Cell Physiol., 2016. 57(8): p. 1689-706
    [PMID:27335347]
  3. Yuan W, et al.
    A cis cold memory element and a trans epigenome reader mediate Polycomb silencing of FLC by vernalization in Arabidopsis.
    Nat. Genet., 2016. 48(12): p. 1527-1534
    [PMID:27819666]
  4. Li C,Cui Y
    A DNA element that remembers winter.
    Nat. Genet., 2016. 48(12): p. 1451-1452
    [PMID:27898079]